Chemotherapy remains the frontline therapy for systemic malignancies. However, drug development has been severely hampered by an inability to efficiently elucidate mechanisms of drug action. This limits both the development of modified compounds with improved efficacy and the capability to predict mechanisms of drug resistance and select optimal patient populations for a given agent. Although drug-target interactions have traditionally been examined using biochemical approaches (Sato, S., et al., Chem. Biol. 17, 616-623 (2010)), a number of genetic strategies have been developed to identify pathways targeted by uncharacterized small molecules. A well-established genetic approach to drug classification is chemogenomic profiling in yeast (Giaever, G, et al. Nat. Genet, 21, 278-283 (1999); Giaever, G, et al. Proc, Natl. Acad, Sci. USA 101, 793-798 (2004); Lum, P. Y. et al, Cell 116, 121-137 (2004); Parsons, A, B, et al. Nat. Bioteehnol. 22, 62-69 (2004); Hillenmeyer, M. E. et al. Science 320, 362-365 (2008)). In this approach, bar-coded yeast deletion strains are exposed to select agents, and genotype-dependent drug sensitivity is used to identify genes and pathways affected by a given drug, as well as to develop a response signature that can be compared with other chemical or genetic perturbations (Parsons, A, B, et al. Nat. Bioteehnol. 22, 62-69 (2004); Parsons, A. B. et al. Cell 126, 611-625 (2006); Hillenmeyer, M. E. et al. Genome Biol. 11, R30 (2010)). This approach has proven quite powerful and has been broadly disseminated; however, its efficacy in interrogating cancer chemotherapeutics is limited by the lack of conservation of certain drug targets from yeast to mammals. This is a particular problem in the context of targeted therapeutics, which are frequently directed toward alterations that are specific to mammalian tumors.
More recently, genetic approaches have been developed to examine drug action in mammalian settings. One such approach is to examine drug response in a diverse panel of tumor cell lines (Shoemaller, R. H. Nat. Rev. Cancer 6, 813-823 (2006)). In this case, the pattern of cell line sensitivity and resistance can serve as a signature that defines drug mechanism. Additionally, drug response can be correlated with the presence of specific cancer related alterations, although this analysis can be confounded by the large diversity of alterations present in a given tumor. An alternative approach is to compare the global transcriptional changes induced by test compounds to those induced by known drugs or defined genetic alterations (Hughes. T. R. et al. Cell 102, 109-126 (2000); Gardner, T. S et al., Science 301, 102-105 (2003); Lamb, I. et al. Science 313, 1929-1935 (2006); Hieronymus, H. et al. Cancer Cell, 10, 321-330 (2006)). Gene expression changes are used as signatures that are characteristic of exposure to a given agent or the presence of a specific cellular state, and common expression changes can be used to cluster similar small molecules. Although each of these approaches have yielded important new insights into drug action, these strategies retain a level of technical variability and resource requirement that limits both disseminated use and overall efficacy.
Thus, a need exists for improved methods that screen and characterize drugs.